ImmPort strategies to enhance discoverability of clinical trial data

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Describes strategies for submission of clinical trial data to the NIAID Immunology Database and Analysis Portal in order to advance discoverability, comparability and analysis

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ImmPort strategies to enhance discoverability of clinical trial data

  1. 1. ImmPort: Strategies to Enhance Discoverability of Clinical Trial Data Barry Smith http://ontology.buffalo.edu/smith https://immport.niaid.nih.gov 1
  2. 2. pipeline 2
  3. 3. BISC pipeline PIs, hospitals, biostatisticians … 3
  4. 4. BISC pipeline PIs, hospitals, biostatisticians … 4 Northrop Grumman
  5. 5. BISC pipeline PIs, hospitals, biostatisticians … 5 Northrop Grumman Max & Mindy
  6. 6. BISC pipeline perform study & collect data analyze data (SAS …) submit data to ImmPort process & de-identify, data in ImmPort discover, aggregate, analyze, data in ImmPort
  7. 7. pipeline is siloed by heterogeneous terminologies and standards perform study & collect data analyze data (SAS …) submit data to ImmPort process & de-identify, data in ImmPort discover, aggregate, analyze, data in ImmPort
  8. 8. siloes break discovery, comparability and analysis perform study & collect data analyze data (SAS …) submit data to ImmPort process & de-identify, data in ImmPort discover, compare, analyze, data in ImmPort
  9. 9. 9
  10. 10. 10 76 results; 0 results for ImmPort
  11. 11. how break down terminology-created silo walls? perform study & collect data analyze data (SAS …) submit data to ImmPort process & de-identify, data in ImmPort discover, aggregate, analyze, data in ImmPort standards and software CDISC, SDTM EHRs, ELNs, CTMSs standards and software ImmPort templates MYSQL … 11
  12. 12. Immune-Related Ontologies (examples) Protein Ontology (PRO) Gene Ontology (GO) Cell Ontology (CL) Immune Epitope Ontology Beta Cell Genomics Ontology Infectious Disease Ontology Allergy Ontology Antibody Ontology CDISC2RDF CL+ (for CyTOF) Cytokine Ontology Immunology Ontology VDJ Ontology http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies 12
  13. 13. these ontologies are already being used by Max and Mindy perform study & compile data analyze data (SAS …) submit data to ImmPort process & de-identify, data in ImmPort discover, aggregate, analyze, data in ImmPort standards and software CDISC, SDTM EHRs, ELNs, CTMSs standards and software ImmPort templates html, SQL .. immune- related ontologies GO, PRO, CL, …
  14. 14. pipeline perform study & compile data analyze data (SAS …) submit data to ImmPort process & de-identify, data in ImmPort discover, aggregate, analyze, data in ImmPort standards and software ImmPort templates html, SQL .. immune-related ontologies GO, PRO, CL, … CDISC2RTF standards and software CDISC, SDTM EHRs, ELNs, CTMSs 14
  15. 15. strategies • FDA-CDISC-CDISC2RDF • LabKey / Electronic Lab Notebook strategy • training submitters and users 15
  16. 16. Rho strategy PIs, hospitals, contract research organizations (CROs): Rho Federal Systems Division Northrop Grumman Max, Mindy 16
  17. 17. ImmPort: Training and Strategy Meeting Rho Federal Systems Division, Chapel Hill, Oct. 9-10 – to provide assistance to actual and potential submitters of data to ImmPort – to enable interaction between submitters and those charged with managing ImmPort – to improve discoverability and usability of data from ImmPort Speakers Ashley Xia (NIAID) Barry Smith (Buffalo / BISC) Jeff Wiser (NG / BISC) David Iklé, John Lim, Karen Kesler (Rho) http://ncorwiki.buffalo.edu/index.php/ImmPort 17
  18. 18. one idea: an ontologically informed CTMS incrementally removing silos through the entire ImmPort pipeline PIs, hospitals, CROs: Rho Federal Systems Division Northrop Grumman Max, Mindy 18
  19. 19. not only would this make life easier for all the participants listed here: PIs, hospitals, CROs: Rho Federal Systems Division Northrop Grumman Max, Mindy, Atul … 19
  20. 20. it would also make ImmPort data discoverable by external researchers PIs, hospitals, CROs Northrop Grumman de-identified patient data 20

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